During a call to Lioness, her cousin Eliza is attacked and kidnapped. The team travels to Brazil to rescue her.

Flesh and Spydah poison Axel with potent venom from a very toxic water spider. As Axel, who is using Jo-Lan to slow down the toxin’s deadly effects, is getting medical attention, Shark is put in charge of the team by Axel himself.

Now, without a base to call home, Paine seeks to use a remote that can control electronic devices to blackmail Landmark City into giving him enough money to rebuild. Lioness's cousin from Brazil, Eliza comes to visit and immediately has Hawk and Shark attracted to her. Axel and Garrett, stumble into a mysterious room of Lee Industries that is off limits to anyone but Lee himself.

When Shark skips out on a fancy party held by Lee on his yacht, he is captured by the villain, Eel. With various sea creatures under his mind-control, Eel sends his "pet" giant squid to sink Lee’s yacht.

Paine steals cyborgs from one of Lee’s factories. Having Spydah duplicate their schematics and create more, Paine now controls his own cyborg army.

The Alpha Teens accompany Hawk, who stars in the movie being filmed, "Radioactive Island", to an island that served as a military testing site. While King’s animalistic nature steals Hawk’s thunder, it also gets the attention of Recombo, a mad scientist who combines different species of animals into one.

Needing a bit of extra intelligence to correct a design flaw (with Hard Light), Mr. Lee takes over the advanced school where King's brother, Duke, attends. The process in which Lee uses to siphon all the students' intelligence into Duke turns him evil and gives him telekinesis.

Lioness' neglectful rocker father comes to visit, hoping to mend fences with his daughter. Meanwhile, Magness is planning a major heist -- at the very concert the team is attending!

Lee, who is acting clingy and parental around the team, equips them with new gear and weaponry to test. At the same time Paine and his henchman Spydah seek to destroy the Landmark City dam. Axel also tells Lioness about his past with Paine.

The Alpha Teens move out of Lee’s R & D physicality and into an abandoned Aquatic Center. Meanwhile, due to a freak accident caused by Axel previously, Paine gains new powers that emit terrible pain through his body which he can transfer to those he touch. With these powers, Spydah and added help from the acrobatic Cannonball Bros., Paine goes to Lee Industries, seeking revenge on Axel Manning.

Paine learns of Nutronium, a chemical that can put an end to his constant pain. He and Spydah seek to steal it with the help of Albert, a dangerous muscle-laden criminal who uses a barbell for a weapon. In the heat of battle with the Alpha Teens, Paine unintentionally mutates Albert into the super-strong giant, Flesh.

King has his eyes set on winning the WWC World Title Belt under the guise as the wrestler Royal Rumble. Paine however, seeks the belt for his own dastardly schemes and hires the rhyming extortionist, Vinnie Rossi to stand in for an injured Flesh. During the WWC battle royal for the title, Vinnie’s lovesickness for Lioness could cost him the match and much more.

Lee introduces the Alpha Teens to the somewhat insecure teenage genius, Garrett. In another scheme to ease his own inner pain, Paine sends Flesh and Spydah to kidnap Dr. Evans, an expert in sound wave research and Garrett’s former professor at Landmark University.

After Spydah is fired by Paine for failing to get a crucial flash drive that was protected by the Alpha Teens, he intends to prove himself to his former boss.

After being stopped by the Alpha Teens once again, Paine enlists the aid of five extreme athletes to take them out once and for all.

Paine receives a letter with a photo of himself, Axel's father and some other people who are crossed out and he also receives a disk from which he is very scared. He wants Axel to guard him and he promises to tell him about his father. Dragon and an army of ninjas kidnap Paine and Axel and his friends go to save him. When they rescue Paine and put him back in jail he gives Axel a picture of his father and a man whos face is burned from the picture.Paine tells Axel that when he finds the person on the picture he will find his answers.

When Mr. Lee breaks Recombo out of prison, he (Recombo) invades the dreams of the A.T.O.M. team.

Paine unleashes a huge hurricane on Landmark City with the Atmospheric Modifier, a device made by Dr. Nimbus, whose family Paine is holding hostage.

When a corrupt cop falsely accuses the Alpha Teens of grand theft auto, they become fugitives of the law. Worse yet, Hawk and King are captured, arrested and sentenced to serve time in the same prison where some of the villains they busted were sent to.

With the Aquatic Center totaled by Paine, Spydah and Tilian collectively, and still trying to find paying jobs, the Alpha Teens make a rundown apartment their new home. Garrett, though may has a solution for their problem. Meanwhile, Lee sends mutant clones of Lioness and King, Firekat and Wrecka respectively to destroy the team.

King takes the team camping in Blue Pines National Park for his birthday. The park however has become nothing as King described it. A vicious mutant, combined of different animals, is loose in the park.

Vinnie "The Mass" Rossi returns -- now a molten magma man -- bringing freak volcanic rifts all over the city. The reason behind his appearance? Lioness. On a side note, the extremeness of Hawk and Shark's snow fun causes $97 million in damages, which the city expects the two to pay.

As Paine plots to steal plutonium from Landmark City’s nuclear power plant, Col. Richter of Landmark City’s law enforcement accuses (with strong video evidence) that Axel stole an armored car filled with money. At the same time, Axel’s father, Sebastian Manning, seems to be alive.

A new airplane is created by a friend of Garrett. However Garrett does not trust him, so Axel is told to check out the plane. When Garrett's friend spots him he is forced to leave. Then the Mu-team arrive to steal the plane, but Axel, Lioness, Shark, King and Hawk stop them. The Mu-team then smash a building and Shark saves the building but gets zapped by an electrical wire and becomes unconscious, meanwhile the Mu-team steal the aeroplane. When Shark awakens he believes himself to be a military person. The team are told to listen to Shark or he may sustain brain damage. Later the Mu-team uses the aeroplane to steal an experimental liquid, and Tilian drinks it making him grow into a giant, but the team defeat them and shark is returned back to normal.

After competing in and completing the reality show, Trackdown, the five contestants, Axel, Hawk, King, Lioness and Shark are offered jobs to test new and experimental vehicles for Mr Lee, Trackdown’s creator and president and founder of Lee Industries, a multi-billion dollar company. The five accept his offer, but when a dangerous criminal mastermind named Paine escapes from prison, Axel has personal interest into helping recapture him.